Molecular characterization of chromosome translocation t(11;18)(q21;q21) and its correlation to carcinogenesis

ABSTRACT

Methods for determining whether a tissue sample or an analogue and/or derivative thereof comprises a cell with a chromosome (11:18) translocation associated with malignancies such as mucosa-associated lymphoid tissue (MALT) lymphomas. The invention further provides insight into a novel mechanism of transformation of primary cells. The mechanism involves expression of a fusion proteinaceous molecule comprising at least apoptosis inhibitor 2 (API2) or a functional part, derivative and/or analogue thereof fused to at least one other proteinaceous molecule. The invention also provides a novel nucleic acid sequence and proteinaceous molecule expressed from the sequence termed “MALT-lymphoma associated Translocation (MLT) protein.”

This application is a continuation of U.S. patent application Ser. No. 09/579,692, filed Mar. 26, 2000, now U.S. Pat. No. 6,689,875, which claims priority from Provisional Patent Application No. 60/138,834, filed Jun. 9, 1999.

BACKGROUND OF THE INVENTION Technical Field

The invention relates to the fields of medicine and diagnostics. More in particular, the invention relates to medicine and the diagnosis of tumors.

Recurrent translocations acquired in a process of transformation are well recognized in nodal B-cell lymphomas. These translocations characterize distinct subtypes of disease and involve genes controlling cell proliferation and apoptosis. BCL2, which suppresses apoptosis, was cloned from the t(14;18)(q21;q32) found in most cases of follicular B-cell lymphoma, whereas translocations involving the BCL1/CyclinDl gene on chromosome 11q13 are seen in nearly all cases of mantle cell lymphoma.¹

By contrast, the genetic mechanisms underlying the genesis and disease progression of extranodal marginal zone B-cell lymphomas of the mucosa-associated lymphoid tissue (MALT) type, a recently recognized distinct subtype of B-cell Non-Hodgkin's Lymphoma's (NHL), are not known.² MALT lymphomas account for five to ten percent of all NHLs and the vast majority of lymphomas arising at extranodal sites. They originate in a setting of chronic inflammation triggered by chronic infection or autoimmune disorders, such as Helicobacter pylori gastritis, Sjögren's syndrome, and Hashimoto's thyroiditis.³ In vitro experiments have shown that H. pylori specific T-cells provide contact-dependent help for the growth of the malignant B-cells of gastric MALT.⁴ The etiological link between low-grade gastric MALT lymphomas and H. pylori infection has also been demonstrated by the regression of some cases with antibiotic therapy.^(5,6) The preferential use of immunoglobulin variable region genes (V_(H)) associated with autoimmune disorders indicates that some MALT lymphomas may arise from autoreactive B-cells.^(7,8)

Since biopsies of these lymphomas are relatively rarely subjected to cytogenetic analysis and their in vitro proliferation is often poor, abnormal karyotypic data have been published for only 46 low-grade MALT lymphomas,⁹⁻¹⁷ 5 extranodal small lymphocytic lymphomas of probable marginal zone origin,¹⁸⁻²⁰ and 23 high-grade gastric MALT lymphomas.^(14,15) Recurrent abnormalities in these cases include trisomies of chromosomes 3, 7, 12, and 18,^(11,17,21) the t(1;14)(p22;q32) which has been described in two cases¹⁷ and the t(11;18)(q21;q21). The t(11;18)(q21;q21) has been detected in 15 out of the 51 low-grade lymphomas arising from various extranodal sites^(9,12,14,18-20) but in none of the high-grade MALT lymphomas or any other subtype of NHL. In the largest cytogenetic series, this translocation has been found in 7 out of 13 cases of low-grade MALT lymphomas with an abnormal karyotype.¹⁴ These data clearly indicate that the t(11;18) represents the most frequent structural abnormality in low-grade MALT lymphomas and seems to specifically characterize this disease entity. An attempt to delineate the breakpoint at 18q21.1 has been described by Akagi et al. (Genes, Chromosomes and Cancer, 24 (1999): 315-321). A detailed characterization, however, is urgently needed.

BRIEF SUMMARY OF THE INVENTION

In one aspect, the present invention provides a detailed molecular genetic characterization of the 11q21 and 18q21 breakpoint regions in MALT lymphomas characterized by the t(11;18)(q21;q21). The invention further identifies that the API2 gene, also known as c-IAP2,²² HIAPI²³ and MIHC,²⁴ an inhibitor of apoptosis, and a novel gene on 18q21, named MLT, are rearranged in this translocation. The invention also identifies that truncation of the API2 gene distal to its three BIR domains and fusion of this truncated gene with the carboxy-terminal region of MLT may lead to increased inhibition of apoptosis and thereby confer a survival benefit to MALT type B-cell lymphomas. In other words, the present invention discloses that, surprisingly, truncation of the API2 gene and fusion to the new MLT gene is crucial for the development of MALT type B-cell lymphomas.

In one aspect, the invention teaches that the t(11;18)(q21;q21) associated with extranodal marginal zone B-cell lymphomas of the MALT type results in the expression of a chimeric transcript fusing 5′-API2 on chromosome 11 to 3′-MLT on chromosome 18. The occurrence of the t(11;18) translocation in not less than 17 out of 51 published cases of low-grade MALT lymphomas^(9,12,14,18-20) including the two cases described herein, along with its presence as the sole cytogenetic abnormality in 16 out of the 17 reported cases, indicates that the t(11;18) represents one of the main recurrent, disease-specific translocations in NHL.

Several observations point to the API2-MLT fusion as the oncogenic lesion underlying the t(11;18). The chimeric cDNA was cloned from two independent tumors. In one case, the genomic breakpoints were also cloned and the structure of both genes and the localization of the breakpoints are in agreement with the expression of the fusion transcript. The cryptic deletion of the 3′ part of API2 in case 1 precludes the expression of a reciprocal MLT-API2 transcript in this case. As a result of the deletion, the 5′-end of the MLT gene is fused to the 5′-end of the MMP20 gene on the der(18). As both genes are present on opposite strands of the DNA, no MLT-MMP20 transcript is expressed. Furthermore, FISH experiments with PACs for respectively MLT, API2 and MMP20 clearly suggest that, in case 2, a balanced translocation occurred not involving a break in the MMP20 gene, further arguing against any significance of the MLT-MMP20 fusion.

API2 belongs to the family of inhibitors of apoptosis proteins (“IAP”), which play an evolutionary conserved role in regulating programmed cell death in diverse species (International Patent Application WO 97/06182 to Rothe and Goeddel). The IAP genes were first identified in baculoviruses in which they demonstrated an ability to suppress the host cell apoptotic response to viral infection.³³ Subsequently, five human IAP relatives have been described: NIAP, API1 (also known as cIAP1, HIAP2, MIHB), API2 (cIAP2, HIAP1, MIHC), XIAP-hILP and survivin.^(22-24,34-37) The common structural features of all IAP family members is a motif termed baculovirus IAP repeat (“BIR”) occurring in one to three copies, a caspase recruitment domain or CARD³⁰ located between the BIR domain(s) and a carboxy-terminal zinc binding RING finger domain³¹ that is present in all IAPs with the exception of NIAP and survivin. The human API1 and API2 proteins were originally identified as proteins that are recruited to the cytosolic domain of the tumor necrosis factor (TNF) receptor II via their association with the TNF-associated factor (TRAF) proteins, TRAF-1 and TRAF-2,²² and have been subsequently shown to suppress different apoptotic pathways by inhibiting distinct caspases, such as caspase-3, caspase-7, and pro-caspase-9.^(35,38)

The function of the novel MLT gene (also known as “MALT1”) located on chromosome 18q21 is not yet known. Its closest homologue is a hypothetical C. elegans gene. The carboxy-terminal part of this gene is characterized by the presence two Ig-like C2-type domains and a domain similar to the murine Ig gamma chain VDJ4 sequence (Accession no. M13070). The C2 domains are only present in the longer fusion cDNA of case 2 and thus probably have no functional significance in the tumor.

The molecular mechanism of action of the API2-MLT fusion remains to be elucidated. Without being limited by theory, it is hypothesized that the fusion protein resulting from the t(11;18) may lead to increased inhibition of apoptosis and thereby confer a survival advantage to MALT lymphomas and allow antigen-independent proliferation. Indeed, MALT lymphomas have been shown to display low levels of apoptosis³⁹ and to escape from FAS-mediated apoptosis⁴⁰ and about 20% of low-grade MALT lymphomas do not respond to H. pylori eradication therapy.⁶ The truncation of API2 after the BIR domains could release their anti-apoptotic effects from regulation by the CARD and RING domains. Recent studies have shown that the BIR domain-containing regions of API1 and API2 are sufficient for inhibition of caspases and suppression of apoptosis.³⁵ The BIR domains of one of the Drosophila homologues (“DIAP1”) were demonstrated to suppress apoptosis in the Drosophila eye disk, whereas the full-length protein exhibited less activity. Moreover, transgenic flies over-expressing the RING domain alone exhibited increased cell death in the eye, suggesting that the RING domain may act as a negative regulator of cell death suppression in some instances.³⁴ On the other hand, a specific role for the carboxy-terminal MLT domain is suggested by its consistent presence in the fusion and by the recurrency of the t(11;18) in MALT lymphoma. This is supported by the observation that full-length API1 and API2 were somewhat more potent in caspase inactivation than constructs lacking the RING domain.³⁵ It is possible that the presence of the MLT domain would stabilize the fusion protein, increase its affinity for protein interaction or influence its subcellular localization, thereby modulating its interactions with other proteins.

The mechanism of gene deregulation by the t(11;18) differs from that seen in most of the B-cell lymphoma-associated translocations, which involve one of the immunoglobulin loci on 14q32, 2p12, or 22q11 and lead to deregulated expression of the incoming oncogene due to the proximity of potent B-cell transcriptional enhancers within the immunoglobulin loci.⁴¹ In this case, the expression of the fusion gene is driven from the promoter of its 5′ partner, API2. This agrees with the observation that API2 mRNA is highly expressed in adult lymphoid tissues, including spleen, thymus, and peripheral blood lymphocytes, and also in fetal lung and kidney.²³ It is also interesting to note that the IAP family member survivin is strongly expressed in apoptosis-regulated human fetal tissues, but not in terminally differentiated adult tissues.⁴² Survivin becomes prominently expressed in transformed cell lines and in most human cancers. Survivin expression was also found in 50% of high-grade NHL (centroblastic, immunoblastic) but not in low-grade lymphomas (lymphocytic).³⁷

At the genomic level, the rearrangements appear to be heterogeneous. The breakpoint in MLT occurred in two different introns for both cases. In the API2 gene the breakpoint occurred in the same intron for both cases, but it was associated with the deletion of the 3′-end of the gene in only one tumor. The cytogenetic analysis of MALT lymphoma is often hampered by their poor proliferation in vitro. However, the physical maps and the genomic clones that the present invention teaches allow the development of a wide variety of sensitive detection methods for this rearrangement, such as but not limited to interphase FISH assays and assays based on the specific amplification of nucleic acid encompassing the t(11:18) breakpoint. Alternatively, the fusion mRNA or the fusion protein provides new molecular targets for diagnosis.

In one aspect, the invention provides a method for determining whether a tissue sample or an analogue and/or derivative thereof comprises a cell with a chromosome (11:18) translocation associated with malignancies such as MALT lymphomas, the method comprising subjecting nucleic acid from the sample to an amplification reaction using a primer that is complementary to a nucleic acid sequence which in humans lies on chromosome 11 region q21-22.3 and a primer that is complementary to a nucleic acid sequence which in humans lies on chromosome 18 region q21.1-22, and determining the presence of any amplified product. Preferably, the tissue sample is taken from a human individual. Preferably, the individual is suffering from or at risk of suffering from a disease.

The nucleic acid may comprise chromosomal DNA, RNA or any other type of nucleic acid. With the knowledge of the region in which the (11:18) translocation occurs, a person skilled in the art is capable of developing specific nucleic acid amplification methods that allow the unambiguous detection of the translocation in a tissue sample. Such assays may be developed based on nucleic acid sequence information presented here. However, it is clear that using the teachings of the present invention, i.e., the identification of the breakpoint and the methods and means to do so, additional nucleic acid sequence information on the region surrounding the breakpoint can be obtained and the use of such sequence information for the development of detection assays for the translocation falls within the scope of the present invention. The term “complementary primer” means a primer that can hybridize to another sequence under relatively mild hybridization conditions, i.e., hybridization conditions that allow nucleic acids with sequences with some mismatches to hybridize to each other. The number of mismatches among others determines the specificity and the efficiency of polymerization. A complementary primer should comprise not more than 30% mismatches, preferably not more than 20% and more preferably not more than 10%. Preferably, the primer does not comprise mismatches.

Amplification methods that may be used in a method of the invention include but are not limited to polymerase chain reaction, NASBA and intracellular PCR.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

FIG. 1: Cytogenetics and YAC characterization of the t(11;18).

FIG. 2A-B: Molecular structure of the t(11;18). The genomic structure of the t(11;18) is shown in panel A. In the center, the MLT gene is shown as the darkly shaded area on the normal 18q; API2 and MMP20 are shown respectively as an open rectangle and a light grey rectangle on the normal 11q (not drawn to scale). Below each gene, the PAC isolated for this gene is shown. For PAC 152M5, the positions of the different BamHI fragments used for FISH experiments are indicated. On top, the rearrangement in case 1 is illustrated: the der(11) fuses the 5′ end of API2 to the 3′ end of MLT, while on the der(18), as a result from the cryptic deletion of chromosome 11, the 5′ end of MLT is fused to the 5′ end of MMP20. The transcriptional orientation of each gene is indicated by an arrow below each chromosome, showing that on the der(18), MLT and MMP20 do have an opposite transcriptional orientation. The genomic fusion fragments which were cloned respectively from the der(11) and the der(18) are indicated by the double lines. Below the rearrangement of case 2 is shown: the der(11) fuses 5′ API2 to 3′ MLT. The breakpoint in API2 is identical to the one in case 1; the breakpoint in MLT occurred upstream of the breakpoint in case 1 (see 2B). FISH experiments suggest that the der(18) is the balanced reciprocal of the der(11). The localizations of all breakpoints are indicated on the normal chromosomes by open triangles.

Panel B illustrates the structure of the different fusion cDNAs. On top, the structure of API2 is shown with 3 amino-terminal BIR domains separated from the carboxy-terminal RING domain by a CARD domain. The API2 cDNA is truncated after the third BIR domain and fused in frame to MLT the nucleotides shown below the structure correspond to nucleotides 1434 to 1446 and 2029 to 2045 of SEQ ID NO:7, the amino acids corresponds to 438 to 441 (the serine) and 637 to 641 of SEQ ID NO:8, (the case 1 junction produces a codon for Asparagine (N)). As a result of the heterogeneity of the genomic breakpoints in case 2, 582 additional nucleotides, encoding two Ig-like C2 domains of MLT, are present in this fusion. An Ig gamma VDJ4-like sequence in MLT is shown by a cross-hatched box. The sequence and translation of the different junction fragments is shown underneath each cDNA; in case 1 the nucleotides correspond to nucleotides 1434 to 1446 fused to nucleotides 2029 to 2045 of SEQ ID NO:7 and the amino acids correspond to 438 to 441 (the serine) and 637 to 641 of SEQ ID NO:8 (the junction produces a codon for Asparagine (N)); in case 2 the nucleotides correspond to nucleotides 1434 through 1463 of SEQ ID NO:7 and amino acids 438 through 447 of SEQ ID NO:8.

FIG. 3A-D: FISH Mapping of the chromosome 11 and 18 breakpoints. A: the hybridization signals of YAC 921 F3 and the BamHI fragment H of PAC 152M5 are both split by the translocation in case 1. Signals of both probes are visible on the derivative chromosomes 11 and 18. B: in case 2, fragment D of PAC 152M5 shows split signals. The centromeric probes for chromosomes 11 and 18 appear. C: in case 1, PAC 532024 is seen on the normal chromosome 11 and on the derivative chromosome 11 (C), whereas this probe is split by the translocation in case 2 (D). The signals of the centromeric probes are shown.

FIG. 4A-B: Molecular characterization of the fusions. (A) shows the API2-MLT products obtained by RT-PCR from case 1 and case 2. (B) shows the Southern blot detecting the rearranged EcoRI fragments of case 1. The probes were derived from an 8 kb EcoRI clone from chromosome 18 spanning the breakpoint (see FIG. 2A center). Lane 1 shows hybridization with the probe derived proximally to the breakpoint; lane 2 shows hybridization with the probe derived distally to the breakpoint. The arrow shows the normal 8 kb EcoRI fragment; the arrowheads show the chimeric fragments.

FIG. 5A-E: Sequence of the API2-MLT chimeric cDNA SEQ ID NO:7.

FIG. 6A-B: A) Genomic structure of the MLT gene. A (partial) BamHI and (B) restriction map of PAC 1 52M5 is depicted. The sizes of ordered BamHI fragments are indicated; the last BamHI site of the first lane corresponds to the first one on the second lane. Solid rectangles represent the different MLT exons; their respective number is marked above. Solid lines delineate the MLT introns; their estimated size is specified underneath. The unique SacII site is present in exon 1 of MLT; the size of the fragments obtained after NotI/SacII digestion are indicated. B) Features of API2, MLT and observed API2-MLT fusions of the five cases characterized are shown. API2 contains three amino-terminal BIR domains separated from the carboxy-terminal RING domain by a CARD domain. The arrow indicates the position of the API2 breakpoint observed in all cases, between exon 7 and exon 8. MLT harbors two Ig-like C2 domains and an Ig gamma VDJ4-like sequence.

FIG. 7A-B: A) The chromosome 11 breakpoints on the der(11) and sequence features of intron 7 of API2. Numbering is according to Acc. No. AF178945. B) Schematic representation of the genomic structure of the API2-MLT and MLT-API2 fusion fragments in five cases (not drawn to scale). Grey and black boxes represent API2 and MLT exons respectively; white boxes represent repetitive elements. Solid black bars define deletions associated with the t(11;18) translocation. When known, the distance between the breakpoint and MLT exons is indicated. Abbreviations for repetitive elements (matching repeat # repeat class/family): AluSx # SINE/Alu (Sx), AluJo # SINE/Alu (Jo), AluSg/x # SINE/Alu (Sg/x), AluY # SINE/Alu (Y), L2 # LINE/L2, MIR # SINE/MIR, FLAM_A # SINE/Alu, L1MC3 # LINE/L1.

DETAILED DESCRIPTION OF THE INVENTION

In a preferred embodiment, the amplified product comprises a linked nucleic acid comprising at least part of nucleic acid encoding a MALT-Lymphoma associated Translocation (MLT) protein and at least part of nucleic acid encoding apoptosis inhibitor 2 (API2).

In a preferred embodiment, the tissue sample comprises a lymphocyte, preferably an activated lymphocyte. In a preferred embodiment, the tissue sample comprises digestive tract cells and/or stomach cells.

In another aspect, the invention provides an isolated and/or recombinant nucleic acid encoding a proteinaceous molecule comprising at least API2 or a functional part, derivative and/or analogue thereof fused to at least one other proteinaceous molecule. The other proteinaceous molecule may be any proteinaceous molecule. Preferably, the other proteinaceous molecule comprises a MALT-Lymphoma associated Translocation (MLT) protein or a functional part, derivative and/or analogue thereof. Preferably, the nucleic acid molecule comprises in humans a sequence as depicted in FIG. 5 or a functional part, derivative and/or analogue thereof.

A nucleic acid of the invention may further comprise other nucleic acid. Other nucleic acid may facilitate cloning or amplification in bacteria. Preferably, the other nucleic acid comprises nucleic acid corresponding in humans to chromosome 11 region q21-22.3 or a functional part, derivative and/or analogue thereof. In this way, the nucleic acid has advantageous properties for FISH analysis. Preferably, the other nucleic acid comprises nucleic acid corresponding in humans to chromosome 18 region q21.1-22 or a functional part, derivative and/or analogue thereof. In this way, the nucleic acid has advantageous properties for FISH analysis.

The invention further provides a proteinaceous molecule encoded by a nucleic acid of the invention, or a functional part, derivative and/or analogue thereof. The protein may be advantageously used for the at least in part transforming a primary cell, preferably a B-cell and thus enabling and/or facilitating the generation of in vitro growing cell derivatives of the cell. One method of providing a cell with a proteinaceous molecule is through providing the cell with an expressible nucleic acid encoding the proteinaceous molecule and culturing the cell to obtain expression of the proteinaceous molecule. Preferably, the proteinaceous molecule comprises a sequence that, in humans, is a sequence as depicted in FIG. 5, or a functional part, derivative and/or analogue thereof.

In another aspect, the invention provides an isolated recombinant nucleic acid encoding an MLT protein that, in humans, comprises a sequence as depicted in FIG. 5 or a functional part, derivative and/or analogue thereof. The invention further provides an MLT protein encoded by a nucleic acid mentioned heretofore or a functional part, derivative and/or analogue thereof.

The invention further provides an antibody specific for a proteinaceous molecule according to the invention. It is clear to the person skilled in the art that antibodies can be generated in many ways once a suitable antigen has been identified. Antibodies can be generated through, for instance, the immunization of an animal or human with a proteinaceous molecule of the invention. Alternatively, suitable peptides can be generated and used using standard protocols used in the art to generate antibodies in a mammal. However, antibodies can also be generated completely artificially from, for instance, libraries of synthetic antibodies, single-chain antibodies, FAB fragment libraries, etc. Suitable antibodies may be isolated from such libraries through techniques known in the art. Furthermore, for the purpose of this invention, any proteinaceous molecule capable of binding to a proteinaceous molecule of the invention is considered an antibody.

In another aspect, the invention provides the use of a nucleic acid of the invention and/or an antibody of the invention as a probe. The term “probe” refers to a means for detection. A nucleic acid of the invention may be used as a probe, for instance but not limited to, for hybridization to Southern Blot DNA of cells or for in situ hybridization of cells to determine the presence of DNA complementary to the nucleic acid. Information regarding the presence of such DNA may be used for determining the presence or absence of cells comprising the (11:18) translocation. Similarly, an antibody of the invention may be used for the determination of cells expressing a proteinaceous molecule of the invention.

In another aspect, the invention provides a method for at least in part improving an immune response against an antigen comprising providing an immune cell comprising an immune property specific for the antigen with an expressible nucleic acid of the invention.

In yet another aspect, the invention provides a method for at least in part preventing apoptosis in a cell comprising providing the cell with an expressible nucleic acid of the invention.

In yet another aspect, the invention provides a nucleic delivery vehicle comprising a nucleic acid according to the invention. Preferably, the nucleic acid delivery vehicle comprises a virus particle, preferably an adenovirus particle, an adeno-associated virus particle and/or a retrovirus particle.

In yet another aspect, the invention provides a cell comprising a nucleic acid according to the invention and/or a proteinaceous molecule according to the invention.

In yet another aspect, the invention provides a transgenic animal comprising a nucleic acid according to the invention. The transgenic animal can be any known non-human animal and is preferably a mouse as is exemplified further.

The invention is further explained by the use of the following, illustrative Examples.

EXAMPLES 1. Characterization of the 11q21 and 18q21 Translocation and Cloning of the Fusion Genes

Material and Methods

Tumor Specimens

Two cases of low-grade extranodal gastrointestinal MALT lymphomas displaying the t(11;18)(q21;q21) were selected from the files of the Center for Human Genetics, University of Leuven, Belgium, and the Department of Hematology, University of Salamanca, Spain, based on the availability of metaphase spreads and frozen tumor tissue. Case 1 presented with an extended multifocal gastrointestinal MALT lymphoma involving the stomach, the small and large bowel, and the mesenteric lymph nodes. Case 2 was diagnosed with a gastric MALT lymphoma with secondary involvement of the spleen, the bone marrow, and the peripheral blood. Both cases revealed H. pylori-associated gastritis and showed the typical morphology and immunophenotype of marginal zone B-cell lymphomas of MALT type including the characteristic tumor cell composition, extension of the marginal zones by tumor cells, follicular colonization, lymphoepithelial lesions, expression of IgM, CD 19, CD2O, Igk light chain restriction, and negativity for CD5, CD 10, and CD23.²

Cytogenetic Analysis

Cytogenetic analysis was performed as described¹¹ utilizing tissue of a small bowel biopsy (case 1) and the spleen specimen (case 2). Both cases showed the t(11;18)(q21;q21) as the sole cytogenetic abnormality (case 1: 46,XY,t(11;18)(q21;q21) [17]/46,XY [3]; case 2: 46,XX,t(11;18)(q21;q21) [6]/46,X [14]). Fluorescence in situ hybridization (FISH) was performed as previously described.²⁵ Chromosomes 11 and 18 were identified by cohybridization with chromosome 11 (pLC11A) and 18 (L1.84) specific alpha-satellite probes in combination with G-banding using 4,6-diamidino-2-phenylindole-dihydrochloride (DAPI) counterstain.

Yeast Artificial Chromosome (YAC) Clones

YAC clones derived from the Centre dEtude du Polymorphism Human (CEPH) human mega YAC library were selected from the YAC contig reported by Chumakov et al.²⁶ and data obtained from the Whitehead Institute/MIT Center for Genome Research. In addition, YAC A1 53A6 hybridizing to the BCL2 gene located at 18q21²⁷ and a probe specific for the MLL gene on 11q23 (Oncor, Gaithersburg, Md.) were used. Human YAC inserts were selectively amplified using Alu-polymerase chain reaction (PCR).²⁸ In order to confirm their cytogenetic position and to determine the relative order of the YAC clones, pairs of differentially labeled YACs were hybridized to normal metaphase spreads obtained from PHA-stimulated peripheral blood lymphocytes of a healthy donor.

P1 Artificial Chromosome (PAC) and Plasmid Clones

PAC clones were isolated by screening high-density filters from the RPCI libraries with ³²P-labeled probes. A walking strategy was used to extend the map. PAC end-fragments were rescued using a vectorette ligation approach.²⁹ The presence of the STS in the relevant PACs was confirmed by PCR and each PAC was analyzed by FISH on normal metaphase spreads.

BamHI subclones of PAC 152M5 were generated by ligation of gel-purified fragments in pUC18 (Pharmacia Biotech, Uppsala, Sweden) and transformation into XL10-gold cells (Stratagene, La Jolla, Calif.). A BamHI restriction map was generated by comparing the sequence of the ends of the BamHI fragments to the sequence of random 1 kb subclones selected for containing the BamHI restriction sites. To generate random subclones of PAC 152M5, DNA was sheared by sonication and the fraction around 1 kb was gel-purified (Qiaquick Gel Extraction, Qiagen), blunted and ligated in pUC18, and transformed into XL1-blue cells.

Reverse Transcriptase (RT)-PCR and Cloning

Total RNA was extracted from respectively tumor-infiltrated gastrointestinal and splenic tissue using the Trizol Reagent (Life Technologies, Inc., Rockville, Md.). First strand cDNA was reverse transcribed from 1 μg of total RNA with Murine Moloney Leukemia Virus reverse transcriptase (Life Technologies, Inc., Rockville, Md.) according to standard procedures using a random hexamer primer. After size fractionation on Microspin S-400 HR columns (Pharmacia Biotech), a poly-A tail was added to the first strand cDNA with dATP and terminal deoxynucleotidyl transferase (Boehringer Mannheim, Mannheim, Germany). Double-stranded cDNA was then generated using standard procedures with primer R2T8 (5′ CCAGTGAGCAGAGTGACGAGGACTCGAGCTCAAGCTTTTTTTT 3′ (SEQ ID NO:1)). Nested PCR was performed respectively using primers MLTr1 (5′ CCTTCTGCAACTTCATCCAG 3′ (SEQ ID NO:2)) and MLTr2 (5′ ATGGATTTGGAGCATCAACG 3′ (SEQ ID NO:3)) in combination with primers R2F1 (5′ CCAGTGAGCAGAGTGACG 3′ (SEQ ID NO:4)) and R2F2 (5′ GAGGACTCGAGCTCAAGC 3′ (SEQ ID NO:5)). Amplification products were cloned in pGEM T-easy (Promega, Madison, Wis.).

The API2-MLT fusion was confirmed by RT-PCR on patient RNA using the Titan RT-PCR system (Boehringer Mannheim) with primers API2fl (5′ CCAAGTGGTTTCCAAGGTGT 3′ (SEQ ID NO:6)) and MLTr2 and by sequence analysis of the cloned amplification products. A partial MLT cDNA was isolated by 3′ RACE on cDNA of patient 1. Several overlapping clones were analyzed to obtain the 3′ end sequences of MLT (Genbank accession no. AF 130356).

Results

FISH Characterization of the 11q21 and 18q21 Translocation

Twelve YACs derived from the chromosomal region 11q12-22.3 and the MLL probe were hybridized to metaphase spreads of case 1. FIG. 1 shows their relative position in relation to the t(11;18) breakpoints. The hybridization signals of YACs 906C5 and 921F3 were split by the translocation. Subsequent analysis showed that YACs 906C5 and 921F3 also spanned the translocation breakpoint of case 2.

From the 9 YACs assigned to 18q21.1-22, five hybridized centromeric and two (including A153A6 containing the BCL2 gene) telomeric to the translocation breakpoint (see FIG. 1). The hybridization signals of YACs 949B6 and 817C6 were split by the translocation in both cases. YAC 949B6 contains 3 ordered STSs (cen-D18S887-D18S1055-D18S1129-tel). FISH experiments with PAC clones isolated for these STSs positioned the chromosome 18 breakpoint in case 1 between D18S1055 and D18S1129. A walking strategy initiated from both markers led to the identification of PAC 205G9 and 152M5, which were shown to be split by the t(11;18) in both cases. The breakpoints were further narrowed down by FISH analysis with BamHI fragments subcloned from PAC 152M5 (FIG. 2A). In case 1, fragment H was split by the translocation, whereas in case 2, the breakpoint could be mapped to fragment D (FIGS. 3A-D).

Cloning of the Fusion Genes

In order to identify genes on chromosome 18q in the vicinity of the breakpoints, the sequences derived from short random subclones from the BamHI fragments D, B, H and F were compared to the nucleotide databases. Subclone F24, mapping telomeric to the breakpoint, contained a 178 bp fragment identical to a single EST (IMAGE cDNA clone 1420842, GenBank accession no. AA826328) that resembles a hypothetical Caenorhabditis elegans gene (F22D3.6, Acc. No. U28993). The presence of canonical 5′ and 3′ splice sequences flanking the 178 bp suggested that this represented an exon of a human gene. A second exon with similarity to the same C. elegans gene product was predicted by computer analysis of subclone B9, located centromerically to the breakpoint in case 1. RT-PCR experiments confirmed that both exons were part of the same human transcript and indicated the disruption of this gene (named MLT for MALT-Lymphoma associated Translocation) by the translocation in case 1.

To identify an eventual chromosome 11 fusion partner for MLT, cDNA transcribed from RNA of case 1 was then used in 5′ RACE experiments with two nested primers (MLTr1 and r2) derived from MLT sequences telomeric to the breakpoint. The amplification products were cloned and eight clones with an average insert length of 800 bp were sequenced. Five clones contained only MLT sequences. The three remaining clones showed a fusion of MLT sequences to the 5′ part of the API2 gene, an inhibitor of apoptosis mapped to chromosome 11q22. The API2 protein contains three copies of the baculovirus IAP repeat (BIR) at its amino-terminus and a caspase recruitment domain or CARD³⁰ followed by a carboxy-terminal zinc binding RING finger domain.³¹ The chimeric API2-MLT transcript contains base pairs 1-1446 of API2 (Genbank accession no. L49432) fused in frame with bp 583 of the partial MLT cDNA (Genbank accession no. AF130356). At the protein level, the first 441 AA of API2, containing the 3 BIR domains, are fused to the carboxy-terminal part of MLT (FIG. 2B).

Primers derived from the API2 and MLT cDNA sequences (M&M) were then used to confirm this fusion directly by RT-PCR. An amplification product with the expected size (445 bp) and sequence was obtained for patient 1, confirming the existence of the chimeric API2-MLT transcript. In contrast, using the same primers, a 1000 bp RT-PCR product was obtained with the RNA sample of the second patient (FIG. 4A). Sequence analysis of the cloned product again confirmed an API2-MLT fusion with a continuous open reading frame. The breakpoint in the API2 gene occurred at the same position as described for patient 1. The chimeric cDNA, however, contained an additional 582 bp MLT sequence in agreement with the more centromeric localization of the 18q breakpoint in this case as defined by FISH (FIG. 2B).

To complete the sequence of the chimeric mRNA, 3′ RACE experiments were performed. The consensus cDNA sequences for both API2/MLT fusions are shown in FIG. 5.

Absence of a Reciprocal MLT-API2 Transcript

To analyze the genomic events leading to the expression of a chimeric API2-MLT transcript, we cloned the genomic breakpoints of case 1. To this aim, an 8 kb EcoRI fragment spanning the breakpoint was subcloned from fragment H. Southern hybridization with the 5′ and the 3′ end fragments of this clone detected rearranged EcoRI fragments of respectively 6 kb containing the 5′ end of MLT and 10 kb containing the 3′ end of MLT (FIG. 4B). Long-distance inverse PCR³² was used to amplify the genomic chromosome 11 sequences present in both chimeric fragments and PAC clones corresponding to these chromosome 11 sequences were isolated. To our surprise, two independent sets of PAC clones were obtained. PAC 532024 was isolated using chromosome 11 sequences derived from the der(11). This PAC was shown to contain the 5′ end of API2. FISH experiments with this PAC yielded signals on the normal 11 and the der(11) of case 1. PAC 49A7, obtained with chromosome 11 sequences derived from the der(18), however, did not contain API2 and sequencing showed that this clone contained the MMP20 gene instead (FIG. 2B). FISH experiments with this clone on case 1 resulted in fluorescent signals on the normal 11 and the der(18). Taken together, these data show that, in case 1, the t(11;18) is associated with a cryptic deletion of chromosome 11 sequences distal to the breakpoint, resulting in the absence of an MLT-API2 fusion. These data are in agreement with a localization of the MMP gene cluster telomeric to API2. As the exact distance is not known, we cannot estimate the size of the deletion. Sequencing of the der(18) fusion fragment showed that the MLT gene and the MMP20 gene are on opposite strands of the genome, thereby excluding the expression of an MLT-MMP20 transcript. FISH experiments on case 2 detected a signal for the PAC 532024 on the normal 11, the der(11) and the der(18) consistent with the occurrence of a balanced translocation and a breakpoint in API2. PAC 49A7 yielded fluorescent signals on the normal 11 and the der(18) consistent with the localization of the MMP20 gene distally to API2.

2. Evaluation of the Oncogenic Properties of the API2-MLT Fusion

Two strategies are applied to evaluate the oncogenic properties of the API2-MLT fusion in vivo.

In a first approach, we generate via a bone marrow transplant (“BMT”) mice that express the API2-MLT fusion in their bone marrow cells. Lethally irradiated recipient mice are rescued by transplantation with donor bone marrow that are earlier retrovirally infected with a construct that expresses the API2-MLT fusion protein.

In a second approach, the API2-MLT fusion is introduced in a germline of mice through a human chromosomal vector (HCV). After incorporation of an API2-MLT fusion construct in the HCV via Cre-mediated homologous recombination in hamster cells, the vector is shuffled via microcell-mediated chromosome transfer to mouse ES cells for the generation of transchromosomal (transgenic) mice. B-cell specific expression of the API2-MLT fusion protein is achieved by using a B-cell specific promoter or by removal of a repressor element via a recombinase-mediated system driven by a B-cell specific promoter.

The mice models are used to assess the role of antigen triggering in the development and growth of gastric MALT lymphomas by infection with Helicobacter felis. Mice developing lymphoma provide the appropriate model to evaluate antibiotic therapies and therapies based on immune responses to the fusion protein.

3. Structure of the MLT Gene and Molecular Characterization of the Genomic Breakpoint Junctions in the t(11;18)(q21;q21) of Marginal Zone B-cell Lymphomas of MALT Type

The present example relates to the characterization of the genomic organization of the MLT gene. The information is used to amplify the genomic breakpoint junctions for five MALT-type lymphomas with t(11;18)(q21;q21). Sequences near the breakpoint junctions do not yield evidence for the participation of site-specific recombinases or Alu-mediated homologous recombination in the generation of the t(11;18). Clustering of the breakpoints in intron 7 of API2 and the consistency of “in-frame” API2-MLT fusions therefore point to a selective advantage associated with these fusions which leads to their clonal outgrowth.

Materials and Methods

Patients

Five patients with gastric marginal zone B-cell lymphoma of MALT-type were investigated. The t(11;18) was confirmed by RT-PCR analysis for the API2-MLT fusion transcript (Baens et al. 2000). Cases 4 and 1 are cases 1 and 2 respectively of a previous study (Dierlamm et al. 1999). The features of the API2-MLT fusions for these five cases are depicted in FIG. 6B. Genomic DNA was extracted by using a standard isolation procedure (Sambrook et al. 1989) from 5 sections of 25 microns thick, taken from a frozen tissue block comprising the lymphoma.

The Genomic Structure of MLT

A fetal kidney cDNA library in λgt11 was screened with a 5′ MLT probe to determine the full open reading frame of the MLT gene. MLT cDNAs for the entire open reading frame were used as probes on high-density filters containing 1 kb subclones of PAC 152M5. Purified PAC DNA was sonicated and the ends were blunted by successive treatment with respectively T4 DNA polymerase (AP Biotech, Uppsala, Sweden) and Klenow DNA polymerase (AP Biotech) in the presence of the 4 dNTPs. The fraction between 800 and 1500 bp was gel-purified (Qiaquick Gel Extraction, Qiagen, Hilden, Germany) and cloned into pUC18, linearized with SmaI and dephosphorylated (AP Biotech). Subclones identified by the MLT cDNA probes were sequenced to determine the exon-intron junctions. A vectorette PCR approach (Riley et al. 1990) was applied to amplify exon-intron boundaries absent in the subclone library.

Nucleotide sequencing reactions were carried out by dideoxynucleotide chain-termination with FITC-dATP or fluorescently labeled primers and analyzed on an Automated Laser Fluorescence sequencer (AP Biotech). Sequences were aligned with the Seqman software (DNAstar Inc.). Repeatmasker software developed by the University of Washington was used to identify repetitive elements.

Characterization of the Genomic API2-MLT and MLT-API2 Fusion Fragments

Nested or heminested amplification was performed using the Expand Long Template PCR System according to the manufacturer's recommendations (Roche Diagnostics, Mannheim, Del.). Primers used for amplification are summarized in Table 2. PCR amplification products were gel-purified (Qiaquick Gel Extraction, Qiagen), phosphorylated with T4 polynucleotide kinase (AP Biotech) and sonicated, and the fraction between 800 and 1500 bp was gel purified and cloned in pUC18/SmaI/BAP (AP Biotech). Intron 7 of API2 was amplified using primers API2-1374f and API2-1546r with as template DNA of PAC 523024, containing the API2 gene. Subcloning and sequencing was performed as described above. The genomic API2-MLT and MLT-MMP20 fusion fragments of case 4 were characterized in a previous study (Dierlamm et al. 1999).

Results

The Genomic Structure of the MLT Gene

The present invention discloses an MLT consensus cDNA sequence of 2491 bp (Genbank Accession number AF130356). A fetal kidney cDNA library was screened with a 5′ cDNA probe and two hybridizing clones were identified. Sequence analysis revealed additional 5′ sequences with an “in frame” ATG start codon at position 165 (Genbank Accession number AF130356). To determine the genomic organization of MLT, we generated a 1 kb subclone library of PAC 152M5 containing the MLT gene. Southern hybridizations confirmed the presence of 5′ and 3′ MLT sequences in this PAC clone. MLT cDNAs were used as probes on high-density filters containing the 1 kb subclones of PAC 152M5. Sequence analysis of hybridizing clones yielded the flanking intron sequences for all exons except exon 14 (3′ acceptor of preceding intron missing). A vectorette PCR approach (Riley et al. 1990) was applied to characterize the missing boundary for exon 14. Base pairs 1-373 of the consensus cDNA sequence belong to exon 1 and show a high GC content (78%) with 48 CpG dinucleotides and recognition sequences for several rare cutting restriction enzymes (SacII, NarI, NaeI). In total, 17 exons all flanked by canonical splice donor and acceptor sites were identified (Table 1). The size of the introns was estimated by long range PCR with exon specific primers and/or restriction mapping. It shows that the MLT gene is approximately 80 kb in size (Table 1 and FIG. 6A).

The Genomic Breakpoint Junctions for 5 MALT-Type Lymphomas with t(11;18)

Five marginal zone B-cell lymphomas of MALT-type were selected from 11 cases identified with an API2-MLT fusion as part of large screening of gastric lymphomas (Baens et al. 2000). All 11 cases had their chromosome 11 breakpoint in the 5 kb intron between exon 7 and 8 of API2 (exon numbering according to Young et al. 1999). The genomic structure of MLT shows that the chromosome 18 breakpoint in these cases occurs upstream of exon 3, 5, 8 or 9 respectively and that the intron sizes permit amplification of the genomic fusion fragments using API2 and MLT exon primers (Table 2). Genomic DNA extracted from a frozen tissue block comprising the lymphoma was used as a template. Nested or heminested amplification yielded the genomic API2-MLT and MLT-API2 amplification products for all cases, except for case 2 where no MLT-API2 fragment could be amplified (Table 2). All fragments were partially sequenced until the breakpoint junctions were detected by comparison with the intron 7 sequence of API2 (Acc. No. AF178945). The sequence of the latter was determined from a 5 kb PCR fragment amplified from PAC 532024 with primers for exon 7 and 8 of API2 (Table 2). Sequences fused to API2 were then used to screen high-density filters containing the 1 kb subclones of PAC 152M5 to obtain the MLT sequences flanking the breakpoint.

The genomic breakpoints on chromosome 11 are scattered in intron 7 of API2 (FIG. 7A). Sequence analysis of the der(18) junction showed that the MLT gene is fused to MMP20 (Matrix MetalloProteinase 20). However, both genes are transcribed in opposite orientations which exclude the expression of an MLT-MMP20 fusion transcript. Sequence analysis of the API2-MLT fusion further indicated a deletion (2.3 kb) of chromosome 18 sequences (FIG. 7B). Deletions of chromosome 18 sequences were also observed for case 5 (350 bp) and case 3 (around 5 kb), in the latter case simultaneously with a small deletion of chromosome 11 sequences (53 bp) (FIG. 7B). No MLT-API2 amplification product was obtained for case 2. Based on the position of the der(11) breakpoint, the expected fragment is at most 5 kb and thus well within amplification range, which suggests a deletion of chromosome 11 sequences including exon 8 of API2. The latter is supported by FISH experiments with PAC 166G16 for API2 which yielded hybridization signals on the normal chromosome 11 and the der(11), but not the der(18). Identical FISH results were previously obtained for case 4 where the translocation was associated with a deletion of chromosome 11 sequences (>200 kb), which explains the absence of hybridization signals on the der(18) (Dierlamm et al. 1999). Only the translocation in case 1 is not associated with chromosomal loss (FIG. 7B).

Characteristic Sequences Near the Breakpoints

Computer-based FINDPATTERN® searches were performed to identify sequence motifs that might reveal a common mechanism for DNA breakage and rejoining. In lymphoid neoplasms, the presence of heptamer-nonamer recombination signals at or near the breakpoints suggests the involvement of V(D)J recombinase activity in the illegitimate recombination events leading to these translocations (Tycko and Sklar 1990). We did not find appropriate antigen receptor gene-like signals within the chromosome 11 and 18 sequences flanking the breakpoint junctions. The absence of non-template N nucleotides at the fusion junctions, characteristic for V(D)J recombination, further argues against its involvement.

Several other sequence motifs that could potentially infer recombination or genetic instability leading to chromosomal translocation have been reported, such as the DNA topoisomerase II binding and cleavage site (Negrini et al. 1993; Gu et al. 1994; Domer et al. 1995) χ-like sequences (Wyatt et al. 1992), the translin-binding consensus sequence (Jaeger et al. 1993; Aoki et al. 1995) and alternating polypurine-polypyrimidine stretches (Boehm et al. 1989; Thandla et al. 1999; Wiemels and Greaves 1999; Thandla et al. 1999; Wiemels and Greaves 1999). None of these sites were consistently present near the breakpoint junctions. An 18/18 bp match for the topoisomerase II consensus sequence was only observed for case 1. Degenerated sequences (15 to 16 bp match on 18) were identified on one or both participating chromosomes for 4 out of 5 cases, but their position relative to the breakpoint does not imply any causality. Based on the same criteria, a recombination event mediated by χ-like elements could be excluded. Furthermore, no regions homologous to the Translin-binding consensus sequence or with alternating polypurine/polypyrimidine stretches were apparent.

Homologous recombination between human Alu repeats located on the same or different chromosomes has been reported to cause chromosomal translocations (Jeffs et al. 1998; Strout et al. 1998). Alu repeats are also often observed in the vicinity of breakpoints and it is speculated that their mutual attraction juxtaposes these different chromosomal regions and in this way facilitates recurrent rearrangements between them (Obata et al. 1999). Repetitive sequences near the breakpoint junctions were identified using REPEATMASKER® and are summarized in FIGS. 7A and B. In two cases (4 and 5), the breakpoint in intron 7 of API2 occurred in an AluSx repeat, although a different one, but no AluSx sequences were found close to the breakpoint site on chromosome 18. Case 1 had a breakpoint in a copy of an AluSx repeat on chromosome 18 but the break in intron 7 of API2 was 558 bp upstream of the second AluSx repeat. For the remaining 2 cases (2, 3), AluSx repeats were detected close to the breakpoints on both chromosomes. For case 2, only the der(11) was characterized as no MLT-API2 amplification product was obtained. The breakpoint was located 400 bp downstream from an AluSx repeat on chromosome 11 and 52 bp upstream from an AluSx repeat in intron 4 of MLT. The der(11) breakpoint for case 3 was located 291 bp upstream from an AluSx repeat on chromosome 11 and 160 bp downstream from an AluSx on chromosome 18. Due to deletions affecting both chromosomes, the der(18) breakpoint was situated 238 bp upstream from an AluSx on chromosome 11 and in an AluY repeat in intron 4 of the MLT gene (FIG. 7B).

TABLE 2 PCR primers used for long distance amplification of API2-MLT and MLT-API2 genomic fusions. API2-MLT Primer Locus Size (kb) Sequence 1r API2-1266f Exon 7 5′-ATTAATGCTGCCGTGGAAAT (SEQ ID NO: 41) 2r API2-1301f Exon 7 5′-CCTGGTAAAACAGACAGTTCAGA (SEQ ID NO: 42) case 1 MLT-i2r1 Intron 5′-CAGGTGGTGGATAACGTGGAGTTT (SEQ ID NO: 43) 1r MLT-i2r2 2 8 2r Intron 5′-CACAAATCTGCCTGGCCAGAGAAG (SEQ ID NO: 44) 2 case 2/3 MLT-984r Exon 5 5′-GCTTTTTGGTCTCATGTGTTAATG (SEQ ID NO: 45) 1r MLT-929r Exon 5 10/7 2r 5′-AATAGGGCTTCCAACAGCAA (SEQ ID NO: 46) case 4 MLT-1147r Exon 8 5 5′-GGATGACCAAGATTATTTAATTCA (SEQ ID NO: 47) 1-2r case 5 MLT-1181r Exon 9 ~1   5′-CAAAGGCTGGTCAGTTGTTTG (SEQ ID NO: 48) 1-2r MLT-API2 Primer Locus Sequence 1r API2-1684r Exon 8 5′-AACACAGCTTCAGCTTCTTGC (SEQ ID NO: 49) 2r API2-1546r Exon 8 5′-TTAATAATTCCGGCAGTTAGTAGAC (SEQ ID NO: 50) case 1 MLT-i2f1 Intron 5′-GGTTGAGCTTGGAAAGACAAAGG (SEQ ID NO: 51) 1r 2 2r MLT-i2f2 Intron 6 5′-ACCTGATGCACTCTATTTTACGTGG (SEQ ID NO: 52) 2 case 2/3 MLT-717f Exon 4 5′-GCAGGCTTTTATGTCTGTCG (SEQ ID NO: 53) 1r 2r MLT-757f Exon 4   2.2 5′-TTGAATTCAGCCAGTGGTCA (SEQ ID NO: 54) case 4 previously 0.65 (Dierlamm done et al, 1999) case 5 MLT-i8f1 Intron 5′-CTTTTGTAAATAGCCACCACTAAGATT (SEQ ID NO: 55) 1r 8 2r MLT-i8f2 Intron 5 5′-TTCCCACAATTCAGGGAGTACCAAA (SEQ ID NO: 56) 8 1r: first round primer 2r: second round primer 1-2r: first and second round primer

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1. An isolated nucleotide sequence consisting of a nucleic acid encoding SEQ ID NO:60.
 2. The isolated nucleotide sequence of claim 1, wherein said nucleotide sequence is fluorescently labeled.
 3. An isolated nucleic acid consisting of the complement of the isolated nucleotide sequence of claim
 1. 4. The isolated nucleic acid of claim 3, wherein said nucleic acid is fluorescently labeled.
 5. An isolated RNA encoding amino acids 528-566 of SEQ ID NO:60.
 6. A cDNA encoding amino acids 528-566 of SEQ ID NO:60.
 7. A recombinant virus encoding amino acids 528-566 of SEQ ID NO:60. 